Oh, I am sorry. Lack of time as always, and nobody interested in the solution.

I checked the script "/scripts/sysup"and found that it verified "/etc/cpupdate.conf". So the only thing was left is to fix "Update preferences" via WHM. I switched "DarkORB Package Updates" and "Security Package Updates" to "manual updates only" (it was set to "Never Update") and "/scripts/sysup" updated everything.